Mid-term 1

Question 1

What is a Ribozyme?

Answer 1

an RNA molecule that acts like a protein enzyme (in catalyzing biochemical reactions).
a catalytic RNA molecule with a well defined tertiary structure that enables it to catalyze a chemical reaction.

Question 2

What is an intrinsically disordered protein (IDP)?

Answer 2

a protein that lacks a fixed or ordered three-dimensional structure.[2][3][4] Meaning that the SECONDARY SRUCTURE IS NOT FIXED IDPs cover a spectrum of states from fully unstructured to partially structured and include random coils, (pre-)molten globules, and large multi-domain proteins connected by flexible linkers

Question 3

What is an “Open Reading Frame” ORF?

Answer 3

an open reading frame is the part of a reading frame that has the ability to be translated. An ORF is a continuous stretch of codons that begins with a start codon and ends at a stop codon. An ATG codon within the ORF may indicate where translation starts.

Question 4

What does it mean to say that the genetic code is “degenerate”?

Answer 4

meaning it includes redundancies (the codons of 4 nucleic bases translate not into 4x4x4=64 amino acids but only into 20). This redundancy is an important safeguard in biology.

Question 5

What does it mean to say that Protein Coding regions of DNA evolve as a result of protein function?

Answer 5

In other words, the function of the protein is selected based on the environment and its physiochemical viability. Meaning: Evolution is a change in DNA based on the function of proteins.

Question 6

What are Homologous genes?

Answer 6

genes that arise from a common ancestral DNA sequence (vertically RELATED genes).

• Orthologous genes diverged after a speciation event, while paralogous genes diverge from one another within a species.
• ANALOGOUS is opposed to HOMOLOGOUS. Sequences may seem very similar, so it may be assumed that they come from a common ancestor, but analogous sequences arise similar but independently, not being passed down from a common ancestors

Question 7

Why is it easier to detect homology in proteins rather than the coding DNA?

Answer 7

Function matters more in evolution than the sequence.
• Redundancy in the genetic code makes it more difficult for insightful alignments.
• Therefore, if you are studying a known protein coding regions, it is more insightful to align protein sequences rather than the corresponding DNA, but not always…

Question 8

What is the relationship between sequence similarity and homology?

Answer 8

similarity is not the same as homology (coming up). Similarity only implies homology

Question 9

Methods for Pairwise Sequence Alignment

Answer 9

• Dot-matrix • Display all possible sequence alignments as diagonals on the matrix • Find short patterns and detect inverted repeats • Does not show the actual alignment. • Computationally efficient.
• Dynamic programming • Most used alignment method. Needleman-Wunsch for global alignment / Smith-Waterman as local alignment. Smith-Waterman was used for human genome• Became necessary for dealing with gapped alignments • Dynamic programming is guaranteed to get the optimal alignment • Can be very computationally expensive
• Word / k-tuple method • Search for identical short stretches of sequences (words/k-tuples) • Join these words into an alignment by dynamic programming • FASTA/BLAST are also heuristic

Question 10

What is the difference between a local and a global alignments ?

Answer 10

in a local alignment, you try to match your query with a substring (a portion) of your subject (reference). Whereas in a global alignment you perform an end to end alignment with the subject (and therefore as von mises said, you may end up with a lot of gaps in global alignment if the sizes of query and subject are dissimilar

Question 11

What is the difference between Pyrimidines and purines?

Answer 11

Pyrimidines: thymine and cytosine -ONE RING PYRIMIDINES

purines (Adenine and Guanine) – TWO RING PURINES

Question 12

What are the functional classes of RNA?

Answer 12

• Viral genomic RNA
• Messenger RNA (mRNA)
• Transfer-RNA (tRNA)
• Ribosomal-RNA (rRNA)
• Catalytic-RNAs (ribozymes)
• Regulatory or non-coding RNAs (ncRNAs)
• Small nuclear RNAs (snRNAs)
• Long noncoding RNAs
• Ribonucleoproteins
• Riboswitches

Question 13

Describe the RNA world hypothesis.

Answer 13

proposes that life based on RNA pre-dates the current world of life based on DNA, RNA and proteins. RNA is able both to store genetic information, like DNA, and to catalyze chemical reactions, like a protein (the “functional RNA” or “Ribozymes” do). It may therefore have supported pre-cellular life and been a major step in the evolution of cellular life.
The RNA world evolved into a world of RNP enzymes (ribonucleoprotein enzymes), such as the ribosome, before giving rise to the DNA, RNA and protein world of today.

Question 14

What is a spliceosome?

Answer 14

a RNP complex containing snRNA and protein subunits that removes introns from a transcribed pre-mRNA segment

Question 15

Describe RNA structure.

Answer 15

RNA molecules usually come as single strands but left in their environment they fold themselves in their secondary structure because of the same hydrogen bonding mechanism. (They don’t look as ordered as DNA, more messy).
Stems (Helices) are formed intra-molecularly.
Loops
Jucntions

Question 16

What forces stabilize protein structure?

Answer 16

Protein structures are stabilized by covalent bonds such as disulfide bond and non-covalent contacts such as van der Waals, electrostatic, hydrogen bond and hydrophobic interactions, the last of which is the driving force for protein folding

Question 17

What is a zwitterion?

Answer 17

dipole molecule
Mostly Amino Acids exist in In the dipolar form, also called zwitterion form. It means that it has one functional group that has a positive charge and one functional group that has a negative electrical charge. making the net charge of the entire molecule zero. Amino acids are the best-known examples of zwitterions.
In the dipolar form the amino group is protonated (-NH3+) and the carboxyl group is deprotonated (-COO-).

Question 18

Which AA is most active?

Answer 18

cystine

Question 19

Types of bonds (in order of strength, strongest to weakest)

Answer 19

• Covalent: they stabilize proteins
• Disulfide: tertiary structure of insulin has disulfide bonds
• Salt bridge:
• Hydrogen bond (with donors and acceptors) – one of the strongest intermolecular attractions, but weaker than a covalent or an ionic bond. Hydrogen bonds are responsible for holding together DNA, proteins, and other macromolecules.
• Long range) electrostatic interaction
• Van der Waals interaction: dipol/dipol interaction.they turn so that the negative sides are away from each other. driven by induced electrical interactions between two or more atoms or molecules that are very close to each other. Van der Waals interaction is the weakest of all intermolecular attractions between molecules.
• Pi-bonds/pi-stacking: noncovalent interactions between aromatic rings. Pi stacking can be “sandwiched” or in T-shape or parallel displaced. Pi elices (and 3/10 helices) are never long

Question 20

What is a clathrate cage?

Answer 20

Water will form a cage around a hydrophobic molecule. If there is another hydrophobic molecule those two cages will be combined in order to minimize the surface area of the cage (because he water rather wants to bind with itself than build more cages).When 2 cages combine water molecules will be released into the free floating water, thus increasing the entropy.
A sphere the smallest amount of surface area in relation to its volume. Therefore oil builds spheres in water, so that the biggest amount of water molecules can get “released”,. can become free floating.

Question 21

Classes of Protein Structure

Answer 21

 Class all-α: the secondary structure is composed entirely of α-helices, with the possible exception of a few isolated β-sheets on the periphery. still 30% of amino acids are (unbound?) in loops and therefore ready for interaction
 Class all-β
 Class α/β: the secondary structure is composed of alternating α-helices and β-strands along the backbone. The β-strands are therefore mostly parallel
 Class α+β: α-helices and β-strands that occur separately along the backbone. The β-strands are therefore mostly antiparallel
 Membrane/cell surface: interact with biological membranes either by inserting into it, or being tethered via a covalently attached lipid. 20–30% of all genes in most genomes encode membrane proteins.
 Multiple domains: Protein Domains: Compact regions of tertiary structure form domains. A given protein can have several domains which serve different functions.
Protein domains are:
independently foldable
have a specific function
are evolutionary preserved
 Small proteins (longest protein: approx. 36,000 residues; has some folded regions but too large to fold completely. proteins with repeats are often not folded)
 Intrinsically disordered proteins
 Coiled-coil proteins
 Designed proteins

Question 22

What is an advantage of quarternary structure?

Answer 22

multiple proteins combined as a quarternary structure: they can combine freely, increasing the number of functions greatly (1 protein can have different structures and different functions. But still they are always together)

Question 23

Why is Folding is considered the “second half of the genetic code” ?

Answer 23

because: genetic code - protein (1st half) protein - function (2nd half) folding determines function

Question 24

Why do proteins fold?

Answer 24

to become functional. An amino acid CHAIN cannot function. Thermodynamic forces are responsible for the folding. The protein goes into an energy minimum state. Hydrophobia and entropy are driving elements of protein folding where the hydrophobic protein domains are being buried inside of a fold. The solvent will gain entropy from the burial of hydrophobic groups (i.e., elimination of water clathrates), and there is enthalpy gain of favorable intra-chain charged, polar, and van der Waals interactions

Question 25

How do proteins fold?

Answer 25

Intermediates are needed.
They fold quickly because they have funnel-shaped energy landscapes that progressively direct the protein towards increasingly low energies as it folds.
Folding is limited by a finding of an optimal pathway throughout the rugged landscape. The structure of the native state is shown at the bottom of the surface. There are ‘key residues’ in the structure; when on the way down these residues have formed their native-like contacts the overall topology of the native fold is established.

Question 26

What are other models of protein folding?

Answer 26

• *Framework model: In the intermediate state there is plenty of (secondary) structure but the intermediate state is not compact Sequential mechanism of protein folding: 3 major stages
• *Hydrophobic collapse model: In the intermediate state there is no (secondary) structure but the intermediate state is compact. What makes sense in this model is that when collapsing the hydrophobic side chains are being buried inside
• *Nucleation condensation: with a collapsing nucleus

Question 27

Structural features of Molten Globule” States

Answer 27

• Some folding intermediates have molten globule structure
• Substantial 2° structure, little 3° structure
• Collapsed state but disordered core accessible to solvent
• Obtained at mild denaturing conditions (low/high pH, high temperature, low/moderate concentrations of strong denaturants)
• Often binds fluorescent dye ANS

Question 28

Structural features of PMG: (Pre Molten Globule State)

Answer 28

• No tertiary structure;
• 20-50% native secondary structure;
• No globular structure;
• More compact than coil, but less compact than MG or N;
• Native-like topology of folded segments;
• Binds ANS

Question 29

What Are the Partially Folded Intermediates for?

Answer 29

To help a polypeptide chain fold

Question 30

How do transmembrane proteins fold?

Answer 30

Need machinery to fold (not spontaneous). Many protein complexes are involved in protein synthesis. The actual production takes place in the ribosomes (including the folding; starts during translation?) inside of the cell. Through the ER translocon the newly synthesized protein is transported across the membrane into the interior of the ER.

Question 31

What are Molecular chaperones ?

Answer 31

proteins that assist the covalent folding or unfolding and the assembly or disassembly of other macromolecular structures (constitute about 10% of all proteins). Many chaperones are heat shock proteins (absorbing heat to shield the new protein from it and thus preventing reaction with the environment instead of folding onto itself?). They prevent partially folded interstate protein from reacting w/others. They are not specific to proteins, work as chaperones for many.

Holdases (prevent folding in order to let interior reactions occur first or in order to go through the membrane first!)
Unfoldases (for misfolded proteins to let them try again)
disaggregase (ATP dependent and non-ATP dependent)

Question 32

Describe the feedback loop nature of protein’s interaction with its environment.

Answer 32

• Protein folding and structure are determined by its interaction with solvent.
• Solvent (water) affects protein structure.
• But in its turn, protein (as any other solute) can affect properties of water.
• This changed water may have different (changed) effects on other proteins (solutes).
• Protein can affect other molecules in solution by changing properties of water, and not by direct interaction.

Question 33

What is An Oligomer?

Answer 33

a polymer whose molecules consist of relatively few repeating units.An oligomeric protein consists of a few of the same or different proteins.

Question 34

Advantages of Oligomeric Proteins?

Answer 34

you can build large proteins, combine them freely, increase functions greatly by combinations. Also if one subunit contains errors it can be excluded from incorporation into the final oligomer. (“quality control”)

Question 35

What are Different Types of Oligomeric Protein Complexes?

Answer 35

• Dimers, trimers, tetramers, etc. Up to 20
• Homo- and hetero-oligomeric complexes (made up of same (homomer) or different (heteromer) protei)
• Obligate and non-obligate oligomers (obligate: functionally obligate; they have to interact/react; they are not stable by themselves; non-obligate are stable by themselves). There exists a continuum between the two states which depends on various conditions (pH, protein concentration).

These criteria/categories also combine “obligate heterodimer, non-obligate heterodimer etc)
• Transient and permanent complexes (transient: weak bonds)
• Two- and three-state complexes
• Fuzzy complexes (IDP does not present a single binding site to its partner but resemble a “binding cloud,” where multiple, almost identical binding sites are dynamically distributed in a diffuse manner.)

Question 36

What are Molecular recognition features (MoRFs)?

Answer 36

small (10-70 residues) intrinsically disordered regions in proteins that undergo a disorder-to-order transition upon binding to their partners

Question 37

Induced folding advantage in signaling?

Answer 37

High specificity combined with low affinity. In signaling you need high specifity but weak interactions because it turns on/off all the time.

Question 38

How to differentiate between 2 and 3 state complexes?

Answer 38

By analyzing surface area and interface area of proteins you can find out if they are ordered (three state oligomers are in the same quadrant) or disordered (large amount of surface area altogether or large amount of interface area compared to surface area)
The values are calculated by dividing the total surface or interface area by the number of residues in the monomer (chain length). There is a clear distinction between ordered and disordered protein structures in the per-residue surface versus interface areas.

Question 39

Examples of proteinaceous membrane-less organelles (PMLOs):

Answer 39

nuclear pores in the nucleus; “stress garnules” in the cytoplasm (and in the mytochondria and chloroplast

• PMLOs are many and are often formed in response to changes in the cellular environment.
• Being typically liquid in nature, these organelles can be described as products of the reversible and highly controlled LLPTs.
• Many of these PMLOs are complex coacervates containing (almost invariantly) intrinsically disordered proteins and often nucleic acids.
• It seems that lack of stable structure in major proteinaceous constituents of these organelles is crucial for the formation of phase-separated droplets.
• The liquid-like properties of phase-separated droplets could facilitate functions of their constituents, which are accumulated within droplets at high concentrations but remain dynamic.

Question 40

The standard protein structure-function paradigm

Answer 40

• Lock & Key (1893-Fischer) & induced fit (1957-Koshland) were based on enzyme catalysis
• Catalysis requires tightest-binding to transition state (1921-Polayni, 1946-Pauling)

***But there were exceptions which were ignored. Different terminology by everybody who came across it made it difficult to realize that other researchers came across the same phenomenon.
There were proteins that you could boil all night and they wouldn’t die.

Question 41

Different levels of order and disorder

Answer 41

(0) No disorder (~30% in PDB);
(1) Disordered N- and C-termini;
(2) Disordered loop;
(3) Disordered linker;
(4) Disordered domain;
(5) Disordered protein with some residual structure;
(6) Wholly disordered, mostly collapsed protein; and
(7) Wholly disordered, mostly extended protein.

Question 42

Structural heterogeneity of Disorder

Answer 42

order to disorder continuous spectrum

Nevertheless they are often categorized as either:
Disordered
compact
molten globular (no tertiary structure but secondary structure intact) or
globular (ordered)

Question 43

decrease of pH: folds IUP(intrinsically unfolded proteins) because:

Answer 43

The effects of low pH are attributed to minimization of the large net negative charge present at neutral pH, thereby decreasing charge-charge intramolecular repulsion and permitting hydrophobic-driven collapse to the partially-folded intermediate

Question 44

Temperature increase induces folding of NUPs because

Answer 44

Natively unfolded proteins become more ordered upon heating due to the increased strength of the hydrophobic interaction at higher temperatures, leading to a stronger hydrophobic driving force for folding

Question 45

Why don’t these proteins fold?

Answer 45

Natively unfolded proteins are an extreme case conformationally unstable proteins. They possess unique combination of low mean hydrophobicity and high mean net charge. High net charge leads to strong electrostatic repulsion, and low hydrophobicity means less driving force for compaction.

Question 46

Different types of disorder predictors

Answer 46

1,) Scales (a particular number assigned to a residue)- many kinds: hydrophobicity, α-helical etc.
Eg. Simple Scale (measures number of contacts per each type of AA. Need a certain number of contacts for a protein to be foldable), Fold-Unfold, Top-IDP Scale
2,) per residue (PONDR® predicts upon single sequences.)
3.) Binary disorder predictors (say if unfolded or “compact” ) - Charge-hydropathy plot and CDF Analysis (Cumulative Distribution Function)
4.) Meta predictors - The prediction results from a collection of predictors can be used as the inputs for another predictor, called a meta-predictor.

Question 47

What are the advantages of using computational tools for data analysis?

Answer 47

speed, low cost, can do from anywhere, and (most importantly) allows us to analyze Big Data

Question 48

What is the relationship between ID and PTM (post translational modification)?

Answer 48

Intrinsic Disorder promotes Post Translational Modifications, be it phosphorylation or other PTMs. ID is crucial for PTMs to happen!
• In addition to phosphorylation, acetylation, ubiquitination, regulated proteolytic cleavage, etc. very often (always?) occur in regions of intrinsic disorder.
• Flexibility of intrinsic disorder facilitates (enables?) binding to the active site of the modifying enzyme.

Question 49

Ramachandran Plot

Answer 49

will tell you in which area your alpha structure or beta structure etc can possibly be present based on electrical conditions allowing for the particular backbone type of that structure)

Question 50

In MoRF’s, One possible advantage of disorder-to-order upon binding is the possibility of high specificity coupled with low affinity. Why?

Answer 50

If a protein undergoes a disorder-to-order transition upon binding, the free energy to organize the disordered region is deducted from the free energies due to the contacts. This can potentially lead to high specificity coupled with low affinity.

Question 51

Why are IDPs so abundant?

Answer 51

Likely to be functional since Intrinsic plasticity might have multiple functional implications
HENCE: New and more general protein structure-function paradigm

Question 52

Is it possible that function of some ordered proteins require partial unfolding?

Answer 52

The phenomenon of dormant disorder is very common.
For example: Light-induced activation of photoactive yellow protein (PYP). It get’s UNFOLDED when hit by light which then leads to the formation of the transient signaling state that interacts with the partner molecules. It needs to unfold to function!
There are other proteins (RV1264) that become unfolded but decreased pH but active with the unfolding
Other activators can be temperature, even mechanical force, interactions which awaken the protein
There are passive factors that can awaken the protein like changes in pH, temperature, light, mechanical force) or
active factors like interaction with membranes, proteins, DNA, RNA, PTM.
Active means the protein interacts. Passive it just happens to it

Question 53

Why IDPs are so common in cell signaling?

Answer 53

In signaling you need a lot of Protein-Protein-Interaction PPI or PPI networks!
Protein-Protein Interaction (PPI) networks typically have a few proteins (hubs) binding to many partners, but with most proteins binding to few partners.
Hubs have Binding promiscuity. They may be extremely disordered:
Standard “lock and key” mechanisms do not readily accommodate binding to multiple partners. This is the “One to many” scenario: 1 hub (often completely disordered) binds to many partners

Question 54

There are different network types:

Answer 54

• Random Network: If you take out 1 the whole network doesn’t work anymore
• Scale-free Network: has some hubs but many “independent” connections. Only if the hub gets hurt does the network suffer but statistically it is much more probable that an end node gets hit

Question 55

Intrinsic disorder in protein-protein interaction networks

Answer 55

• A number of hubs are entirely disordered (example HMGA). The partners were typically, but not always, structured. (One bind to many?)
• A number of hubs contain regions of disorder (example p53). The partners often bind to these disordered regions. (also one to many?)
• Some hubs are structured (example 14-3-3); but their partners are intrinsically disordered. This is the many to one scenario (ex: 14-3-3)

Question 56

What are IDP interaction modes?

Answer 56

are MoRFs, wrappers, penetrators, huggers, grabbers, tweezers, pullers, connectors, coiled coils, chameleons, stackers, dynamic complexes…

Question 57

Protein structure-function continuum: Proteoforms

Answer 57

• The major part of the complexity of the biological machinery is determined by protein variability rather than results from a high number of distinct genes (although the number of protein-coding genes in a human cell is approaching 20,700, the number of functionally different proteins is in a range of a few hundred thousand, at least);
• Typical protein exists as an ensemble of proteoforms; i.e., different molecular forms in which the protein product of a single gene can be found, including changes due to genetic variations, alternatively spliced mRNA and PTMs

Question 58

Functional advantages of disorder in membrane embedded domains.

Answer 58

(A) Disordered proteins can fold into diverse folded states upon binding to ligands.
(B) Equilibrium between a folded and a disordered state provides a general mechanism for switching between an active and an inactive site.
(C) The disordered state is more accessible for posttranslational modifications as a flexible chain can more easily penetrate into the active site.
(D) Disordered chains can act as an entropic spacer between either ligands or protein domains.
(E) It is unclear whether disorder in a membrane protein will lead to faster degradation.

Question 59

The disorder-to-order continuum for soluble and membrane embedded proteins

Answer 59

Soluble proteins can roughly be divided into random coil-like chains, pre-molten globule states with isolated elements of secondary structure, molten globules with fully formed secondary structure but fluctuating tertiary structure, and finally fully folded states. ***Membrane embedded domains can in principle for all but the fully disordered chains as the large number of unsatisfied hydrogen bonds in these states are extremely unfavorable. The states are only stereotypical examples as proteins can fall anywhere on the continuum from disordered to fully folded.

Question 60

The interplay between protein’s folding and energy landscapes

Answer 60

Meaning: a”Normal” protein will get funneled into very few structures (that have very little energy left).Disordered proteins have a wider variety of shapes, a wider funnel (and more energy at the final state). Disordered proteins – anything goes, barely funneled at all (IDP usually have many sub-structures at bottom, different configurations with same Energy)

Question 61

IDPs can be described as various combinations of differently folded regions:

Answer 61

Foldons (independent foldable units of a protein)
Inducible foldons (disordered regions that can fold, at least in part, due to the interaction with binding partners)
Non-foldons (non-foldable protein regions)
Semi-foldons (regions which are always in semi-folded state)
Unfoldons (regions that undergo an order-to-disorder transition to become functional

Question 62

Since the disorder spectrum is continuous what is the best way to analyze disorder?

Answer 62

Use many different tools! Not 1 tool will analyze. IDPs. Use a “wide eye”. Many techniques have been used to analyze structured proteins so using them on disordered ones may give you wrong results. You need to know the tools/techniques in order to interpret the results .For example a molten globule protein may be wrongly categorized as a (structured) dimer due to it’s size (when using gels-filtration chromotoghaphy. Gel has pores.Different sizes will go threw at different speed (smaller ones slower b/c bounces into all pores!) which separates them). Pre-Molten Globule may get wrongly categorized as trimer, (random) coil as higher “grade” oligomer.

Question 63

Decrease in pH folds extended IDPs

Answer 63

Neutral pH has large net negative charge. If you lower the pH there is a minimization of the large net negative charge present at neutral pH, thereby decreasing charge-charge intramolecular repulsion and permitting hydrophobic-driven collapse to the partially-folded intermediate.

Question 64

Temperature increase induces folding of extended IDPs

Answer 64

Heat treatment enriches proteins with high net charge and low hydrophobicity. Natively unfolded proteins have a high charge and low hydrophobicity already.
Natively unfolded proteins become more ordered upon heating due to the increased strength of the hydrophobic interaction at higher temperatures, leading to a stronger hydrophobic driving force for folding
Increasing temperature will kill normal proteins (it will increase their charge and decreases their hydrophobicity) but since IDPs don’t HAVE a structure, it cannot destroy their structure so it doesn’t harm them…

Question 65

IDPs and liquid-liquid phase transitions: Cell as an aqueous multi-phase system

Answer 65

• Eukaryotic cells contain numerous membrane-less organelles, many of which are formed in response to changes in the cellular environment.
• Being typically liquid in nature, these organelles can be described as products of the reversible and highly controlled liquid-liquid phase transitions in biological systems.
• Many of these membrane-less organelles are complex coacervates containing (almost invariantly) intrinsically disordered proteins and often nucleic acids.
• It seems that lack of stable structure in major proteinaceous constituents of these organelles is crucial for the formation of phase-separated droplets.
• The liquid-like properties of phase-separated droplets could facilitate functions of their constituents, which are accumulated within droplets at high concentrations but remain dynamic.
• Eukaryotic cells are inhomogeneously crowded and contain various cellular bodies
• Many of these bodies are proteinaceous membrane-less organelles (PMLOs)
• PMLOs are formed as a result of highly controlled liquid-liquid phase transitions (LLPTs)
• The interior of these condensed liquid droplets represents an overcrowded milieu
• PMLOs are invariantly enriched in intrinsically disordered proteins
• Intrinsic disorder is crucial for formation, disassembly, and functionality of PMLOs

Question 66

IDPs as “edge of chaos” systems

Answer 66

(small changes in env. Can have big diff in how protein reacts – sigmoidal curve)
The edge of chaos is a transition space between order and disorder that is hypothesized to exist within a wide variety of systems. This transition zone is a region of bounded instability that engenders a constant dynamic interplay between order and disorder.

Question 67

Wavy evolution of disorder

Answer 67

Things started out very chaotic/disordered in the RNA World. Then protein’s first job would be to gain stability/a structure for the Ribosome. Things became more structured and stable. Then with the evolution of more complex organisms (eukaryotes) there was a need to introduce some disorder back into the system in order to increase the variety of functions.

Question 68

IDPs more stable or less stable?

Answer 68

Since IDP will degrade faster inside of a cell, they can be looked upon as more unstable. On the other hand they can withstand pH, low pH and other harsh treatment better because they don’t have structure to lose. They can therefore also looked upon as more stable.